thoughts on this script?

[abez]

Just browsing the code nothing jumped out at me. Other than the use of the
label and next.

I'd generally go something like:
while (!$done) {
	$done = 1;
	for () {
		if () {
			$done = 0;
			break; #reloop		
		}

	}
}

Unless I'm reading that next wrong.

On Mon, 22 Jul 2002, nkuipers wrote:

> I'd like to hear anything anyone can say about this...what people would do 
> differently, what they would think to talk about at our meetings after seeing 
> this code, that sort of thing...anything really. I've tried to keep the code 
> properly grouped and documented. Thanks in advance.
> 
> -nathanael
> 
> #Program name: parse_noncoding
> #Author: Nathanael Kuipers (nkuipers at uvic.ca)
> #Date written: July 22, 2002
> #Last updated: July 22, 2002
> #Purpose: parse a blastx xml file and find noncoding queries, then compare 
> them
> # to a list of all queries and extract the corresponding sequences
> #Use: >perl path/parse_noncoding xmlfile masterfile
> 
> #!/usr/bin/perl
> 
> use strict;
> use warnings;
> 
> my $infile1 = shift;
> my $infile2 = shift;
> my $iteration_message1= "No hits found";
> my $iteration_message2= "BLASTSetUpSearch: Unable to calculate 
> Karlin-Altschul";
> 
> my $query_def_prefix = "<BlastOutput_query-def>";
> my $query_def_suffix = "</BlastOutput_query-def>";
> my $query_def = '';
> my @candidates = ();
> 
> my $flag = 0;
> my $sequence = '';
> my %final_list = ();
> 
> open IN, $infile1 or die;
> 
> #
> #parse the xml file and build an array of noncoding-DNA query-IDs
> #
> 
> while (<IN>) {
>   if (/${query_def_prefix}(.*)${query_def_suffix}/) { $query_def = $1 }
>   elsif (/<Iteration_message>${iteration_message1}/) {
>           push @candidates, ">$query_def" }
>   elsif (/<Iteration_message>${iteration_message2}/) {
>           push @candidates, ">$query_def" }
> }
> 
> #
> #compare each noncoding query to a master-list, write matching IDs and
> #corresponding DNA sequences to candidates file. as in the @candidates array,
> #query IDs in the master-file start with >. so the flag is set when 
> #"begin sequence" and unset when "begin new query ID". 
> #
> 
> ROOT:
> for my $i (@candidates) {
>   open IN, $infile2 or die;
>   while (<IN>) {
>     if (/^${i}$/) { $flag = 1 }
>     elsif ($flag && /^[acgtACGT]/) { $sequence .= $_ }
>     elsif ($flag && /^>/) {
>       chomp $sequence;
>       $final_list{$i} = $sequence;
>       $flag = 0;
>       $sequence = '';
>       next ROOT }
>   }
> }
> 
> close IN;
> open OUT, ">>candidates" or die;
> 
> #
> #print sorted hash (kind of)
> #
> 
> my @sorted = sort keys %final_list;
> for (@sorted) {
>   print OUT "$_\n$final_list{$_}\n";
> }
> 
> "I think for my lunch tomorrow I'll make a tuna and pickle triangle bunwich."
> 

-- 
ABeZ------------ ------- ------ - ---------- -- ------------
http://www.indexdirect.com/abez/ Abram Hindle (abez at abez.ca)
---- ------- ----------- ----------- - - ------ --------ABeZ